


Mass Effect: The Story of Daniel Shepard

by thesearcher



Series: Mass Effect: Retold [1]
Category: Mass Effect Trilogy
Genre: F/M
Language: English
Status: In-Progress
Published: 2019-03-22
Updated: 2019-10-16
Packaged: 2019-11-28 04:37:34
Rating: Teen And Up Audiences
Warnings: No Archive Warnings Apply
Chapters: 17
Words: 8,137
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/18203639
Author URL: https://archiveofourown.org/users/thesearcher/pseuds/thesearcher
Summary: A slightly AU story following the story of Daniel Shepard. This story will consist of a short back story, followed by each of the three games (with areas that I make no changes to summarized), then the aftermath, spilling over into Andromeda. Hope everyone enjoys it, I am definitely not the best writer. Please note that I have comment moderation on, and will not approve comments containing foul language.





	1. Prologue/Backstory

**Author's Note:**

> The back story of how Daniel Shepard got to his station on the Normandy, short cause there are not many deviations from the standard.

Service Record:  
Name: Shepard, Daniel  
DOB: April 11, 2154  
DOE: April 11, 2172  
Origin: Spacer  
Defining: War Hero  
Class: Apex  
Age: 29  
Height: 6’3”  
Weight: 200Lb  
Eye Color: Blue  
Hair Color: Brown  
The Alliance recruiting station. Daniel Shepard had dreamed of this day, since he was a child of 7 playing with model ships. Every time one of his parents would tuck him into bed at night. Daniel Shepard was going to be an Alliance Marine, no matter what. Being in the Alliance was in his blood, his father Elijah Shepard and his mother Hannah Shepard (maiden name: Letner) were two of the most decorated Captains in the Alliance fleet. Shepard stood at the entrance of the center, paperwork in hand, filled out in advance, ready to dedicate his life to the Alliance, here went nothing.  
The recruiter looked at Shepard, “Turned 18 today did you, you must be excited to join.” “You have no idea, sir”, Shepard replied, “Been waiting for over a decade.” “Well welcome, everything looks in order with your paperwork, head to the back for your physical.” The man directed him to the back with a point of his thumb. Shepard headed back to the exam room and waited for the doctor. “Hello I am Dr. Endres. How are you doing today?” the older man asked. “Doing pretty good, just want to get going.” “Well, this shouldn’t take long.” About 30 minutes later the doctor looked at Shepard, “Well, everything checks out, did you know you have a large amount of Element Zero in your system? It’s more than I’ve ever seen in a human system before.” “Yes, sir I did know that.”, Shepard replied, “Several doctors I’ve seen think it is due to being on an Ezzo cargo ship for a few years.” That was Shepard’s official line anyway, and a partial truth. No one would ever know how he really got that much Ezzo in his system.  
Shepard arrived at boot camp, they buzzed his hair, what little of it there was, and sent him off to meet his Sergeant. “LISTEN UP MAGGOTS!!”, the sergeant began, “MY NAME IS SERGEANT CARTER! YOU WILL ADDRESS ME AS SARGENT OR SARGE! IF YOU EVER CALL ME SIR I WILL BREAK MY FOOT OFF IN YOUR BUTT! SIR YOU SAVE FOR USELESS PEOPLE!” Shepard had heard of this man, supposedly the toughest of all drill instructors in the Alliance. After the entrance yelling they were sent to their barracks, small thing, barely enough room to move around. Shepard claimed the bunk closest to the door, he always did that, so he could make sure everyone else got out in an emergency. Shepard studied the other recruits with him, memorizing faces, an easy task given his photographic memory, he wanted to make sure he could keep track of them all.One of the other recruits, a man, slightly shorter than Shepard, walked up to him. “Hey, name’s Ryder, you are?” the man asked, “Shepard.”, he replied. “Well, Shepard, nice to meet ya. What do you think of the Sargent?” “I hoped to get Carter when I signed up, heard about him from my parents.” Shepard replied. “Both your parents Alliance?” “Yep.” “Anybody I’ve heard of?” Shepard was already getting tired of this, he didn’t mind telling people who he was, but only people he knew, and Shepard was a common enough surname to get away with it, he decided to be tactful. “Hey, I don’t mind talking but I need to get set up before the Sargent gets in here, you might want to do the same.” “Yeah, you’re right, catch ya later.” The man said as he left to go set up his bunk. Shepard passed the remaining half hour in peace, he set up his bunk and sent off a letter to his parents telling them that he was in, and he had gotten Carter as his Sargent. Then as Shepard finished his letter, almost as if called by the mention of his name, Carter busted in “ATTENTION!”, yelled the corporal. “You ladies are a disgrace, I gave you a full half hour, and you don’t have everything squared away, you won’t last long at al…” Carter paused as he saw Shepard’s gear, “…What have we here, someone who knows what’s going on. What’s your name, Private?” “Shepard, Sargent” he replied curtly. “All of you take a cue from Shepard, this is what I expect to see. Everyone outside in 5 minutes for PT.” The Sargent left, “AT EASE!” the corporal yelled as he followed.  
Boot camp was everything Shepard had hoped and more, but now it got interesting. They had been there for 4 weeks, it was time for the aptitude test, seeing what you were more skilled at, a straight fight, biotics, tech, or some combination of two. Shepard had a surprise in store for them. Shepard had shown that he knew how to handle any weapon they handed him, he had a perfect score on every firing range he had ever been on. What people didn’t know is that his biotic potential was through the roof, due to the high ezeo concentration in his blood. They also didn’t know that he could hack and use tech attacks with the best of them, due to time spent with some quarrian engineers who had hired onto one of the ships his mom was stationed on. The quarrian had told him at the time, “If you can’t crack it kid, it probably can’t be cracked.” The day came, Shepard headed into the tactical range, and started. Picking up the pistol and hitting both the targets that popped up when the pressure plate was released. He proceeded to go through the course, grab the next weapon, and hit the target square in the face, without so much as a second’s hesitation, which was impressive, but even more so when he got to the sniper. The sniper rifle was the last weapon, and the most challenging test, picking it up triggered a series of targets to pop up, 20 of them, meant to be enemies advancing on your crow’s nest, Shepard had hit everyone of the targets before they were even fully up. All without ever looking down the scope for more than a split second. As he exited the course the examiner looked at him, “Well that is the most impressive performance I have ever seen on this course, finished in 45 seconds, and with 100% accuracy. I don’t know how you did it.”, the young woman said, “Anyway, I am going to recommend that you be placed as a soldier, but that will be determined by how you preform on your other tests as well. Good luck, Deadshot.” Shepard thanked the woman and left. At biotic evaluation things went just as well, when they tried to measure Shepard’s biotic power it broke their scales, so they got some systems they had bought from the Asari, top of the line, also busted. Shepard had a level of biotic power never before seen, period. At tech eval, it went swimmingly as well, Shepard hacked the hardest system they had in under 10 seconds, then to show off, hacked the defense mainframe of the base and increased its targeting efficiency by 1500%. When the examiners saw the above perfect score in each area they knew this man was different.  
“Shepard, we weren’t exactly sure what to do with you for a bit”, the Colonel on the reviewing board said, “You see you maxed out and surpassed all the tests we had, Weapons, Biotic, and Tech, you even broke a set of top of the line Asari biotic potential measurement devices.” “Apologizes sir, you can dock my pay for those if you want.” Shepard said, amazed at his accomplishment, he knew his biotics had gotten strong, but to be able to brake a scale built by the ASARI, an entire race of biotics, now that gave him a sense of pride. “That won’t be necessary, however what is necessary is the defining of a new classification for you. You won’t be a soldier, an engineer, an adept, a vanguard, a sentinel, or an infiltrator. The new designation we have for you is Apex. You have achieved the peak of everything we test, you are an apex of humanity, and will be honored as such. We have devised a curriculum for you, it is supposed to be challenging, but I doubt we could come up with something to challenge you.” The Colonel finished up his speech. “Thank you so much, sir, I won’t let you down.” Shepard said biting back a beaming smile. “You’re welcome, and I know you won’t, also thanks for the defense boost, we sent the specs for what you did to all alliance bases with the same system.” “You’re welcome, sir.” “Dismissed.” “Yes, Sir.”  
Boot camp was over, Shepard had graduated as the first ever member of the Apex class. It was exhilarating, he was given his choice of assignments but told them to send him where needed. It wasn’t a very exciting post, but Shepard didn’t care, he was living his dream.  
2176  
Four years, Shepard could hardly believe it, it had been four years since he joined up, and he had loved every minute of it. He hadn’t had anything really exciting happen yet, but he would probably see some excitement soon. Shepard had received the orders last week, he would be transferring to a ship that patrols the edges of the Terminus Systems and was known to encounter pirates and slavers on a semi regular basis. The ship was due back in three weeks, and Shepard had been sent to the ships home port for shore leave till they returned. Shepard had heard of Elysium, no human hadn’t, but he had never been here before. It was beautiful for sure, but it wasn’t a ship, ships would always be Shepard’s home. It was about two weeks before the ship got back, Shepard got up went into his morning routine, 500 each push up, sit-ups, pull-ups, and deep knee bends. Shepard figured he was about ready to go to 550 each, maybe a couple more days. As Shepard went about exploring the city, the air raid sirens started going off, he looked up into the sky and saw hundreds of ships descending to the ground, clearly pirate and merc gangs based on the variance within what he saw of the fleet. Shepard quickly went to work finding where they were landing and fighting, however there were far too many of them for him to take on alone. A week and a half had went by, the resistance Shepard had cobbled together had done well so far, they just had to hold out till the Alliance arrived. Finally, during one of the resistance’s raids they heard a retreat order come over the enemy radios, the Alliance had shown up in force, the fight was over.  
Shepard had been promoted to Lieutenant Commander after Elysium, and given a month’s leave, as well as inductance into the N7 program. Shepard wanted his leave to end, he couldn’t wait to start training. After his leave was up Shepard headed to the villa, a large estate in Rio de Janeiro, where the ICT program was based. The first thing they did was take them out to an asteroid belt and stranded them on one of the asteroids, with only basic gear and no nav data, they said the test would end when the last person ran out of oxygen, and Shepard knew a few tricks to save oxygen. The exercise was over, and Shepard was in, here began the adventure he had been waiting for.  
N7 graduation day, Shepard received full N7 designation, and decided to get a tattoo to commemorate the occasion. It was nothing ostentatious, a circle on the back of his right shoulder, inside which went a gear, a glowing fist, and a gun, all arranged around an N7 logo. Shepard was ready for any assignment they wanted to hand him.  
2183:  
Shepard was back on Arcturus Station, it had been a long time, but he was here to join the crew of a new experimental warship, the Normandy, as the XO. The ships captain was Captain Anderson, Shepard knew of Anderson, very decorated soldier, and first graduate of the N7 program. It was going to be an honor to serve under such a great military man. Shepard had finished his briefing and headed for the ship, he had an XO’s inspection to carry out. The ship was a beauty, combining Turian and Human design aesthetics, seamlessly into a fantastic set-up. The drive core was incredible, and the specs for the stealth system are mindboggling, controlling how the heat generated was dispersed was brilliant. The last thing Shepard had to do before meeting Anderson was to meet the pilot. Flight Lieutenant Jeff “Joker” Moreau, Shepard had heard of this guy. Apparently, he had gotten this position by knocking out the actual pilot and locking him in one of the stations shuttles, then proceeding to finish the set course, and return the ship to berth, all while evading the Arcturus’ security forces. Captain Dillard, Captain Anderson, and the Turian General Invectus observed this, and Dillard wanted Joker thrown into prison, however Invectus and Anderson got him assigned as the ships pilot. After meeting him Shepard saw that Joker lived up to his name, constantly making wise cracks, most being references to the 20th and 21st century popular culture. Shepard was ready for this assignment, shakedown was just a few days away.


	2. Eden Prime

**Notes for the Chapter:**

> Like I said where I don't change stuff the chapters are going to be short.

Eden Prime:  
Shakedown, the day was finally here. The Normandy SR-1 left its dock at Arcturus and headed for the mass relay. Joker broadcasted the actions of approaching the mass relay across the ship as Shepard dodged crew members to get to the bridge. As Shepard entered the bridge the Turian Specter Nihlus was observing Joker’s actions. After the jump Nihlus left and Joker, Kadian, and Shepard discussed why the Council might have sent a Specter on the shakedown run. Their conversation was cut short with Anderson calling the bridge informing them that Shepard was needed in the briefing room. Joker made a comment that kind of ticked the captain off. Shepard went to the briefing room to talk to the Captain, Nihlus was there alone and began asking Shepard questions about the planet they were going to, Eden Prime. Anderson arrived and told Shepard what was really going on. Then the distress call came in, Eden Prime was under attack from an unknown force, and the garrison was losing badly. The Eden Prime mission was a disaster, they lost Jenkins moments in to a Geth Drone. They found a marine by the name of Ashely Williams who had lost her entire team. They found a dead Nihlus and a witness told them that a fellow Turian by the name of Saren had killed him. By the time they finally found the beacon Saren had fled. As Shepard called for evac Ashely got too close to the beacon and it tried to pull her in, Shepard grabbed her and threw her out of the way only to be pulled in himself. Flashes of information, like memories were burned into his brain. Images of synthetics killing people. The beacon exploded and threw Shepard onto the ground knocking him out. Shepard woke up on the Normandy to hear Ashely telling Dr. Chakwas that he was awake, some questions from the Dr. to verify that he was OK, and Anderson ordered the Dr. and Ashely to leave. Ashely apologized as she went out, to which Shepard replied that no apology was necessary. After piecing together what happened Anderson ordered Shepard to go to the bridge and observe Joker dock the ship into the Citadel.


	3. The Citadel

**Notes for the Chapter:**

> Another short chapter. The chapter on Therum will be short as well. The chapter after that will have some actual length to it, and chapters will start happening between missions as well.

Udina, the Council, Shepard was tired of these bureaucratic morons. It had taken Shepard the better part of a week to figure out what he needed to do to get the evidence they needed. The ONLY bright spot is that they picked up some solid team mates along the way. The Turian Garrus Vakarian, the Krogan Urdnot Wrex, and the young Quarian Tali’Zorah nar Rayya all seemed like they were going to be great additions to the crew. The new revelation about these “Reapers” disturbed Shepard to no end, whatever they were they had to be stopped. Shepard felt even more sorry for his commander, Captain Anderson being sidelined and losing his command of the Normandy was a load of crap. Anderson put on a brave face, but Shepard knew he was eaten up inside. You don’t take a ship away from its Captain. Shepard would have to deal with that later. For now, he had a mission. As the Normandy pulled out of dock Shepard gave a rousing speech to the crew and they set course for the Artemis Tau cluster. They needed to find this Liara T’Soni woman, maybe she would know more about why her mother is involved with Saren’s plans.


	4. Therum

**Notes for the Chapter:**

> Another short chapter, no changes here, those are coming though.

Shepard could only think of one word to describe Therum, HOT!!! This planet had to be next door to the literal Biblical Hell to be this hot. Even inside the Mako it was unbearable, and Shepard had trained in Rio, one of the most humid places on Earth. They needed to get T’Soni and get off this place before they all cooked. The Geth were everywhere, hundreds of them, from basic units all the way to Armature class units, Shepard thought that Benezia must really want to get her daughter on board with all this. After freeing Liara they ran into a Krogan Battlemaster and his detachment of Geth, who asked them to surrender, or not as he thought that would be more fun. Liara wasn’t much help in the battle, but they defeated him and ran for the exit, barely getting off planet before the volcano they were in erupted. Back on the Normandy they debriefed, Shepard told Liara what the extinction event she was looking for in Prothean history was, the Reaper invasion. Liara was a bit taken aback, and after being stuck in that shield for so long she was quite tired and went to go rest. The Council contacted Shepard, gave him some warnings about Liara and some basic platitudes about his mission. He was able to keep his cool and finish the conversation in a civil manner. Shepard had always hated politics, and the politicians that came with it.


	5. Noveria

**Notes for the Chapter:**

> Here is where I am starting to make some changes to the story.

Shepard thought it was fitting, they found Liara on a planet next door to literal Hell, and they found her mother on a planet so cold that a yeti wouldn’t want to live on it. And after dealing with that whole mess with the Noveria IA woman Shepard realized he had no cause to complain about the Council any more. The Mako ride was more pleasant, the vehicle clearly handled the cold better than the heat. Peak 15 was a mess, Rachni were everywhere. They found a group of guards who directed them to the hot labs to find Benezia, but the only person there was some Russian scientist who told them they needed to do a neutron purge and kill the crazy Rachni in the hot labs. The Rachni then killed him, Shepard had to take the codes, initiate the purge himself, and run like mad through a massive group of Rachni. When Shepard, Liara, and Tali, returned they found that the guards had abandoned their posts, only to find them in the main area, with orders from Benezia to kill them. Obviously, that didn’t go well for the guards, and they finally reached Benezia, who was with the Rachni queen. The battle against the Asari commandos and Geth troupers was grueling, but in the end, they prevailed and faced down the Asari Matriarch herself. She broke through the control that Saren had over her long enough to give them the information that she had pulled from the Queen, the location of the Mu Relay. She then reverted to Saren’s control and attacked them. They defeated her, and she broke through again. “I can not go on, you will have to stop him Shepard.” It was clear that her injuries were getting the best of her “HOLD ON!!! We’ve got Medi-gel, maybe we can…” “NO!” Benezia cut him off, “He is still in my mind, I am not entirely myself, I never will be again.” “Mother” Liara nearly sobbed out. “Goodnight Little Wing, I will see you again with the dawn. No light they always said there would be a light.” As she started to fade Shepard was shoved aside. “NO!!! I am not losing you mother.” Liara said crying, she applied a couple samples of Medi-gel and looked at Shepard, “I am heading back to the Mako, I will keep her sedated, when we get back to the Normandy, we are going to find a way to fix her.” It was clear this was an order, if Shepard said no he knew he would get his butt thrown across the lab. “OK, Liara, let me figure out what I am going to do about the Queen, and I will head back too. Tali go with her.” “Yes, Shepard.” Tali acknowledged. After the discussion with the Queen Shepard decided to let her go, on the promise that she would stay hidden from the galaxy. The Mako ride back to the central facility was tense, with Liara trying to keep Benezia sedated and Shepard trying to figure out how to tell the Council he let the last Rachni Queen live. The discussion on the Normandy did not go well. Dr. Chakwas was not thrilled about having to keep a powerful biotic in a medically induced coma, and Liara had a few words for her. Shepard was able to calm things down and finish the meeting, but then came the Council report. Needless to say, they were not happy, they jumped down Shepard’s throat about letting the Rachni Queen go first, then even more so about saving Benezia. Shepard barely got a word in edgewise, trying to explain the deal with the Queen, or that he didn’t have a safe say in whether or not to save Benezia. They didn’t want to hear it, they were as pigheaded as ever. Shepard was tempted to have Joker cut the call, but he maintained his demeanor and finished the conversation.


	6. Benezia

Shepard headed to the med bay to check on the situation with Benezia. “How’s your mother doing Liara?” “She is resting well, still in a medically induced coma. Dr. Chakwas, show Shepard the brain scan you did.” Chakwas walked over to the display unit near Benezia’s bed and turned it on. Two brain scans popped up. “I messaged Thessia and asked for an average Asari brain scan for a comparison, they sent me the one on the left. Benezia’s is the one on the right.” Shepard was no medical man, but he could tell there was a distinct difference between the two scans. “By process of elimination we have determined that the shaded areas show Saren’s control. As you can see around 95% of Benezia’s brain is shaded in. He has almost complete control over her, and I have no idea how to do anything with that.” The doctor said, almost defeated. “I have an idea, there is a method we use when a person has amnesia, where some close with them bonds with them and tries to bring up the memories. This method might work here as well.” Liara sounded hopeful. “OK, Liara, go ahead, but doc keep her restrained at all times, and keep her sedated enough that she can’t use her biotics.” “Understood, Commander.” Dr. Chakwas took down the sedative just enough to get the Matriarch conscious. “Liara?” The older Asari said wearily, “Why did you save me?” “Mother,” Liara choked out on the verge of tears, “I wasn’t going to lose you, I think I have a way to help you.” “What is it?” Benezia asked hopeful. “The amnesia technique, I am going to bond with you and try to bring you back through the control.” Benezia’s countenance sunk, “I doubt that will work Little Wing, but you can try.” Liara started the bonding and the brain scan for her mother changed, less of it was shaded not by much but it was progress, after a few minutes though the shading resurged, and Benezia started struggling against the bonds. Dr. Chakwas bumped the sedative back up. Liara sunk, “It didn’t work.” Shepard went over to comfort her, “It was only the first try, and the brain scan changed while you were bonded.” “And some of the change stuck.” Chakwas chimed in, “The scan now says 94.5% of her brain is infected. It is not much but it is progress.” Liara lit up at that. “When can we try again?” “I would wait a while, however long you need to rest plus about 2 hours for your mother.” “OK, then we will try again in about 4 hours.” Liara seemed hopeful again. Shepard hoped this would work, Liara was like a little sister to him, despite the weird age difference.


	7. The Council Calls

Shepard was about to punch in the coordinates for Feros when Joker informed him that the Council was contacting them. He went to the comm room and took the call. They informed him that there was a Salarian STG team that had sent a communication from the planet Vermire and they suspected that it might have something to do with Saren. Shepard thanked them for the information and asked if they had specifics. They said they did not due to the communication being degraded by interference. Shepard added Vermire to his mission list and thanked the Council again, they then said their goodbyes and cut the communication.


	8. Feros

Shepard was reluctant to leave Liara behind this mission, her biotics were a great help, but she was determined to stay with her mother, which Shepard understood. So, this mission was Tali and Wrex for the team. They were greeted by one of the colonists and told that they needed to speak to Fai Dan the leader of the colony. The man was then gunned down by the Geth, who Shepard and his team then dispatched. They fought their way to the colony and found Fai Dan, only to be attacked by the Geth again. They cleared the tower the Geth were coming from and went back. Fai Dan thanked them and gave them the info they needed. He also asked if they could clear the Geth from the tunnels under the colony and directed Shepard to some people working on other problems in the colony. Shepard found that he needed to kill an Alpha Varen to allow the colonists to hunt for food, fix the water system that ran through the tunnels, and find some power cells to fix the power shortage. Thankfully all the problems were in one basic area. So, Shepard and crew were able to fix the water issue, kill the Alpha Varen, get the power cells, and wipe out the Geth in one fell swoop. They then went towards the ExoGeni HQ. On the way they found some ExoGeni researchers hiding in a bunker, and discussed how best to get to the HQ, Shepard also found a man by the name of Gavin Hossle who needed some data retrieved from the HQ as well. When they got to the HQ, they found a woman by the name of Lizbeth Barnum who was trapped there after trying to save some data. She gave them her security card and they headed into the building. They found a VI interface and killed the Krogan trying to access it, then accessed it themselves. It informed them that a creature called a Thorian was living under where they set up the colony, and that it had infected the colonists with a spore that allowed it full control of them. They proceeded to remove the Geth ship from the side of the building by crushing one of its attachment arms with a hanger door. They also managed to retrieve Hossle’s data. On the way out they ran into Lizbeth again, and confronted her about the Thorian, she told them everything and they headed back to the Mako, when they approached the ExoGeni hideout again they heard an argument over the radio, and Lizbeth jumped out of the MOVING Mako and headed for the bunker. Shepard stopped the vehicle and his team followed the woman to the bunker. They talked the head scientist Jeong down from harming Lizbeth’s mother, and were able to figure out a way to possibly neutralize the Thorian’s control of the colonists. The battle was tough, having to be non-lethal was not something Shepard was used to. But the grenades worked, the gas neutralized the spores and knocked out the colonists. As they were raising the covering protecting the entrance to the Thorian’s location Fai Dan showed up. He said the Thorian wanted him to stop Shepard, but he wasn’t going to, and began to bring a gun to his own head. Shepard threw his last nerve gas grenade and it detonated right before Fai Dan pulled the trigger. The Thorian fight was insane, it kept producing a copy of an Asari it had captive, and there were dozens of Thorian Creepers to contend with as well. But they destroyed the creature/plant’s connections to the walls, and it fell to its doom. The Asari that it had captive was released, and she revealed her part in Saren’s plan. She was given to the Thorian in exchange for something called the Cipher, essentially the essence of being Prothean. Shiala, the Asari, gave Shepard the Cipher through a bonding. She then asked what was to be done with her. Shepard let her live and asked her to help the colony get back on its feet. The mission was a success, Shepard had yet another piece of the puzzle he needed to figure out what and where the Conduit was, and the colony was saved. The Council was not as pleased as they should be, they thought that if the colony hadn’t been human that Shepard wouldn’t have tried as hard, and the Salarian Councilor even mentioned that he would have preferred to capture the Thorian alive. Shepard said that even if the colony had been any other race’s he would have done the same, and that trying to capture the Thorian alive would have been probably the stupidest thing anyone alive had ever seen. The Council actually chose to believe Shepard this time and thanked him for his exemplary service. He thanked them and they closed the communication line.


	9. Benezia Part 2

Shepard decided to check up on Benezia again, they had been gone for almost a day and he wanted to see if they had made any progress. “Liara, Dr. Chakwas, how is the patient?” “Much better, take a look.” Chakwas said beaming. The brain scan showed marked improvement, there was a progression photo set up, and in the treatments, they had done Benezia had gone from 95% controlled to around 75% controlled. “It is slow going, but it is progressively easier. Every time it goes down, she is able to remain cogent for longer the next time, and it goes down more.” The doctor continued. “Dr. Chakwas believes that once it is below 50%, we should be able to leave her conscious and bond more often, allowing even faster recovery.” Liara added. Shepard could tell she was tired, but hope and effort, and probably more than a little coffee, was keeping her awake. “That is good to hear, Liara. You two keep up the good work, but Liara get some rest, you look like you haven’t slept in weeks.” Shepard ordered. “I will Shepard, Dr. Chakwas recommended about 15 hours before trying again, so I am going to get some sleep.” Liara confirmed. “Good. I hope this continues to work as well as it has.” Shepard headed to his own bunk as well, they were headed to the Citadel to do some restock, as well as blow off some steam, Heaven knows they needed it.


	10. The Citadel Part 2

Shepard entered the markets to a rather unpleasant sight, Conrad Verner, standing in the same place he had the last two times. Shepard didn’t mind a fan, but this was too much. This time Conrad had a completely ridiculous request, he wanted brought up for Specter consideration. Shepard calmly told him that he could do more on the home front, that people like Conrad and his family were the reason that Shepard kept fighting. Conrad seemed to understand and went home to his wife. The crew relaxed for about a day on the Citadel, Liara never leaving the ship, either being in her bunk or by her mother’s side. They bonded a couple more times and her brain scan showed around 60% control left, they were nearing the tipping point.


	11. Vermire

Shepard punched in the course for Vermire and went to his quarters to study the mission reports the STG team had sent back, as it was a several hour trip. When they arrived, they found a large number of AA guns, so the Normandy dropped the Mako and the team proceeded on the ground. They tore through the Geth and shut down enough guns for the Normandy to head to the camp. When Shepard got there, he found that the Normandy was grounded, and they were not what was expected. Apparently, the commander of this operation, a Captain Kirrahe, had requested a fleet for orbital bombardment, as Saren had a base where he was breeding an army of Krogan, after having found a cure for the Genophage, the semi-sterility plague imposed on the Krogan as punishment for the Krogan Rebellions. Wrex was naturally PO’d that the Salarian’s wanted to destroy the base but Shepard was able to explain that Saren cured the Genophage only to enslave the Krogan for his own uses. This calmed Wrex down, and Shepard said that if he came across the information, he would try to save it. Kirrahe told Shepard the plan and asked for either Ashley or Kaiden to accompany his team, and another needed to go with the makeshift nuke they made. Shepard decided to send Kaiden with the nuke as he had the tech experience necessary to fix anything that went wrong. Ashley went with the STG team, as she was a soldier and they needed her on the front line. The assault went well, Shepard hit the source of every problem that the STG team encountered, and they got into the base. Shepard went to Saren’s main lab and ran into an Asari, Rana Thanoptis, who was helping Saren study Indoctrination. According to her information it is not Saren controlling people it is the ship, Shepard was needless to say confused, but he listened to her explanation. She seemed worried that she might be indoctrinated as well but asked to be let go. Shepard told her that she should stick with them, as they have something that is working against the indoctrination. She agreed and opened the door to Saren’s lab. They found another beacon there, in much better shape, and Shepard activated it. The vision from the first beacon slowed down and made much more sense this time, which wasn’t saying much. On the upper level of the lab they found what they thought to be a VI interface for the Reaper ship that Saren was using. But it turned out that the “ship” was an actual Reaper. It claimed that the label “Reaper” was irrelevant and that they simply were, no beginning and no end. Shepard was taken aback by this, an entire race of AI dedicated to exterminating advanced organic life on a cycle. He wondered what kind of monster designed this. Sovereign cut off the conversation and lifted off. Shepard and team headed back to where they were going to put the nuke. The Normandy dropped off the nuke and Kaiden to set it up, Ashley then contacted them and said she needed backup, Shepard, Wrex, and Tali headed her direction. As they did a Geth drop ship headed toward Kaiden and the nuke, and Shepard had to make a decision, who to save. But he knew he couldn’t afford to lose either member of his team. “Wrex, Tali, head to cover Ashley, I am going back for Kaiden.” He ordered. “Shepard, you can’t possibly handle that many Geth.” Tali nearly cried. “Yes I can Tali, Kaiden will be backing me up. Now go. Get Ashley and the STG team and meet back at the nuke.” The fight was long, Saren showed up and attacked Shepard directly, Shepard was able to make him doubt some of his ideas about the Reapers, but not enough, he still fought, Shepard nearly lost but as the alarm started going off because of the nuke Saren dropped him from the strangle hold and left to board Sovereign. The rest of the team arrived in time to board the Normandy and they got out of the blast zone just in time. The briefing afterward went well, nobody on the crew had actually seen Shepard open up with his skills, but when a person throws an incinerate attack, followed by a warp, and a concussion shot in a fraction of a second, people tend to notice. He told them about his special classification, and his power level. Liara seemed shocked that he had broken Asari biotic potential scales. The conversation went back to the main part of the mission, and Liara told Shepard that maybe with the second beacon’s information, maybe she could make sense of the vision now. The bonding was hard on Liara, she had been expending so much energy on helping her mother. She did however make sense of something. She recognized a planet, Ilos, a Prothean planet almost relegated to myth. Which could only be reached by way of the Mu Relay. The puzzle pieces were all there, and put together, now they needed to get there. Unfortunately, by the time they had gotten to the Genophage labs the cure data had been wiped from the computers and there was nothing to save.


	12. Benezia Part 3

Shepard went to check up on their patient. Liara was asleep by her mother’s side. “How are they doing doc?” Shepard queried. “Well, Liara is getting some much-needed rest, and her mother is asleep, not sedated. She is at 45% controlled now, it should start going faster now.” The doctor said full of hope. Shepard when over to Rana, “And how about our new patient?” “She is not nearly under as much control as Benezia was, her brain scan shows about 65% controlled, so I have her sedated. We will need to bring her out a bit to see who we can contact.” “OK, reduce the sedative enough to make her lucid.” Shepard ordered. “OK, done.” “Where am I?” Rana questioned. “You are on the SSV Normandy, a Human Alliance vessel. We did a brain scan on you and found that you are around 65% indoctrinated.” “I knew it was bad.” She started to cry. “We have something that has been working though. Do you have anyone close to you we can contact, family, a childhood friend, anyone?” Shepard explained/questioned. “I have a sister, she is on Thesia, you could send me to her.” “OK, we will contact her. What is her name?” “Liie, same last name.” “OK, we will contact her and explain to her what must be done. Dr. Chakwas will explain to you, before we put you back under.” Shepard comforted her and left. Shepard sent a communication request to Thessia and was answered immediately. “Hello, Thessia communication hub, how may I help you?” “Yes, I am looking to contact a Liie Thanoptis, her sister told me she lives on Thessia.” “One moment please, I have found her in the system, do you wish to place the call now?” The operator asked. “Yes, please, it is rather important.” The communication was transferred to Liie’s system and Shepard waited for an answer. “Hello, Liie Thanoptis, who is calling?” “This is Commander Shepard of the SSV Normandy. I have your sister Rana on board, and we needed someone close to her to contact.” “WHAT HAPPENED???!!! IS MY BIG SISTER ALRIGHT???!!!” She panicked. “Miss, your sister is physically fine. But mentally is another story. She was working with a man named Saren, studying something called indoctrination. I can’t go into details as it is part of an on-going investigation. But she has fallen under this control.” “WHAT??!! WHO DID IT, I’LL KILL THEM.” The woman was frantic. “Calm down miss, that is not what your sister needs. Have you ever heard of the technique that some Asari use to cure amnesia?” “You mean trying to pull the memories up through bonding with someone close, yes.” “OK, we have another Asari on whom that technique is working to break through the control. If you want, I can give you the details of the process and have your sister sent to you from the Citadel.” “Give me the details, but I will meet you on the Citadel and go through the process there.” “Understood, miss, I will forward you a document with all the necessary information, and will see you on the Citadel.” “Thank you.” They ended the conversation and set course for the Citadel.


	13. Citadel Part 3

Shepard arrived and had Rana moved to the nearest hospital, where they met her sister. “The hospital has everything set up according to your instructions. Are you sure this will work?” “It has been working on the other Asari on our ship so far.” Shepard explained. “Thank you, I will start the process immediately.” Liie left and headed for her sister’s room. Shepard then headed for the Council tower and was greeted by what he thought was going be action, he should have known better. All they were going to do was lock down the relays heading to the Citadel and wait for Saren. Shepard argued passionately against this, but it fell on deaf ears. They even locked out Normandy controls since they landed. Shepard began to hate Udina more and more by the day. Shepard returned to the Normandy and sulked, as there wasn’t much else, he could do. Then Joker chimed in over the intercom and informed him that Captain Anderson wanted to see him. He met Anderson in Flux, the nightclub on the ward. Anderson told Shepard that he had a couple of plans to get the Normandy out of lock down so that Shepard could head to Ilos. They discussed the two plans and decided that it would be best to go to Udina’s office and lift the lock down from there. Shepard and Joker waited with bated breath as they watched for the lock down lift. When it finally came through Joker got them out of there in seconds.


	14. Benezia Cured

Shepard went to the med bay, as the trip to Ilos was a long one, and he wanted to check in on Benezia. He walked in to the med bay and saw the Matriarch sitting up and awake. “Commander Shepard, I want to thank you for saving me.” “Thank your daughter, she gave you the Medi-gel, she came up with the way to bring you back, and she did all the work.” Shepard explained. “Yes, but your encouragement helped her do all that.” Shepard blushed, probably for the first time in his life. He wasn’t used to getting praise for doing his job. “How much control is left?” Shepard asked. “Only about 5%, one more session and that should do it.” Dr. Chakwas explained. “We were actually getting ready to preform it.” Liara stated. “Then I will leave you to it. Liara, does this mean you will be able to accompany to Ilos?” “Yes, it should. I will let you know before we arrive there.”


	15. Ilos

Liara was able to go on this mission, as her mother’s brain scan showed no shaded area left. When they arrived, they had to figure out how best to get to Saren, in the end they decided to do a Mako drop with only 20 meters of space instead of the recommended 100 meters. Joker unsurprisingly pulled it off, but they still had a batch of bad luck. Saren’s Geth had closed a set of blast doors just before they could get through. It took them a good hour, but they finally opened the blast doors and got back to the Mako. The tunnel was well fortified by the Geth, but they fought through and came to a shield which boxed them in. They went down the only exit available to them, on foot. After an elevator ride, they found a VI, named Vigil. It explained the purpose of this planet, it was a secret research facility that was not in the Citadel’s records. Its purpose was to create a small-scale Mass Relay that acted as a back door to the Citadel, it was called the Conduit. Vigil also explained the fact that the Citadel is in fact a Mass Relay that can pull the Reapers from Dark Space beyond the edge of the galaxy, where they hide between harvests. And that the Keepers are sent a signal to activate the Citadel Mass Relay by a vanguard Reaper left behind to observe. It informed them that the last surviving scientists from Ilos went to the Citadel after the war and tampered with the Keepers so that they would not respond to the signal this cycle. They asked Vigil some more questions then headed on. They took the Mako deeper into the tunnel, finally reaching the Conduit. They used the conduit to travel to the Citadel, where they came out near what everyone had thought to be a simple monument of a Mass Relay.


	16. Citadel Invasion

Saren had already overridden the Council’s lockout on the Mass Relays and Sovereign and the Geth fleet had begun their attack. He then locked it down again and began the arms closing, and Sovereign took his opportunity and entered the Citadel to directly take control. When he did that the elevator that Shepard and his team were in stopped. Shepard told them to put their helmets on and shot out the window. They climbed the side of the tower, killing a large number of Geth along the way. They reached the top and were confronted by Saren again. Saren revealed that the doubt that Shepard made him feel convinced him to allow Sovereign to implant him with enhancements, which further strengthened his control over Saren. In the end Shepard was still able to convince Saren that he was being manipulated. He thanked Shepard and shot himself in the head and fell through the glass and into the garden below the Council chambers. Shepard lifted the lock out on the Mass Relays and the Alliance 5th fleet came through. Shepard ordered them to save the Destiny Ascension and the Council. When the Citadel arms opened back up the remains of the fleets attacked Sovereign with all their might, but he still cut through them like a hot knife through butter. Shepard sent his team to check that Saren was in fact dead, to be sure Tali put a second bullet in his head. Then Sovereign took direct control of Saren’s body, activating all his implants, and making him nothing more than a puppet on a string. The fight against the Sovereign controlled Saren was difficult but Shepard pulled out all the stops and they were able to win. Saren’s body disintegrated, and Sovereign realized too late his mistake. All the power he dumped into Saren was rapidly shot back into him, and his shields short circuited. The Alliance fleet was able tear into him and destroy him. One of the smaller pieces of debris crashed into the Council tower and nearly crushed Shepard and his team. When the rescue team arrived Liara and Tali were sure that Shepard was dead, but he climbed up over some wreckage and revealed that he was alive.


	17. Council Invitation

**Notes for the Chapter:**

> The end of the ME1 section of this story. I will start writing the ME2 section soon.

In light of humanity’s contribution to the fight against Sovereign the Council invited humanity to join its ranks. They asked Shepard to recommend a Councilor. He thought about it for a few minutes and then decided to select Anderson. Udina was too power hungry for his tastes, he thought Anderson would be a better fit. The Alliance parliament agreed and set Anderson as the human Council member. Shepard reiterated his commitment to fighting the Reapers and set out to find any more evidence of their attempts to enter the galaxy.


End file.
